DCC | DCC uses output from the STAR read mapper | Genomics library

 by   dieterich-lab Python Version: v0.5.0 License: GPL-3.0

kandi X-RAY | DCC Summary

kandi X-RAY | DCC Summary

DCC is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. DCC has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
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            kandi-support Support

              DCC has a low active ecosystem.
              It has 27 star(s) with 16 fork(s). There are 9 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 29 open issues and 60 have been closed. On average issues are closed in 83 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of DCC is v0.5.0

            kandi-Quality Quality

              DCC has 0 bugs and 0 code smells.

            kandi-Security Security

              DCC has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              DCC code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              DCC is licensed under the GPL-3.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              DCC releases are available to install and integrate.
              Build file is available. You can build the component from source.
              DCC saves you 849 person hours of effort in developing the same functionality from scratch.
              It has 1946 lines of code, 102 functions and 11 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed DCC and discovered the below as its top functions. This is intended to give you an instant insight into DCC implemented functionality, and help decide if they suit your requirements.
            • Wrapper for findcirc
            • Find circular coverage in the junction file
            • Print chimera line
            • Return the genomic distribution of a cigar
            • Finds CircSkip junction files for a given Circus
            • Determine intervals that overlap the DNA sequence
            • Returns a list of junctions for the given CircRNA interval
            • Check if junctions files are empty
            • Check if a file exists
            • Filter circs based on the given circ2filter
            • Fix all the 2 chimera in the input fnames
            • Count the host gene expression based on the given circuit
            • Delete files matching the given pattern
            • Filter the counts based on the read counts
            • Sort the output
            • Annotate a circRNA file
            • Ensures a list of BAM files are sorted
            • Combine coors
            • Map run coordinates to run
            • Determine the order of a GTF file
            • Select genes from gtf file
            • Annotate regions with regions
            • Read a circRNA count file
            • Combine read counts files into a dictionary
            • Remove regions that are not in the given region
            • Convert junction files to bamfile
            Get all kandi verified functions for this library.

            DCC Key Features

            No Key Features are available at this moment for DCC.

            DCC Examples and Code Snippets

            No Code Snippets are available at this moment for DCC.

            Community Discussions

            QUESTION

            Defining a recursive function inside another function in C
            Asked 2022-Mar-18 at 18:13

            I'm trying to write a recursive function (printPath) inside another function (dijkstraSSSP), but it gives me a compiler error.

            When I run gcc dijkstra.c WGraph.c PQueue.c, it compiles just fine. However, when I run dcc -Wall -Werror -std=c11 -o dijkstra dijkstra.c WGraph.c PQueue.c. I got this error:

            ...

            ANSWER

            Answered 2022-Mar-18 at 17:10

            Move the definition of printPath outside of the body of dijkstraSSSP and, to give it access to pred, change it to accept two parameters instead of one. The additional parameter should have type int * and should point to the first element of pred.

            In the call, pass pred for that new parameter. The array pred will be automatically converted to a pointer to its first element.

            Source https://stackoverflow.com/questions/71530625

            QUESTION

            Plotly dash table add rows and update input data
            Asked 2022-Feb-15 at 05:25

            I'm trying to make a dash table based on input data but I'm stucking in add more rows to add new inputs. Actually I read this docs and I know that I can directly input in dash table but I want to update dash table from input.

            Below is my code:

            ...

            ANSWER

            Answered 2022-Feb-15 at 05:25

            tran Try to replace your callback with this callback:

            Source https://stackoverflow.com/questions/71045841

            QUESTION

            R plotly - sankey chart not returned
            Asked 2022-Feb-14 at 02:34

            I am running below code in RStudio, and want to create sankey chart with plotly. code runs without error. but the sankey chart is not displayed. what's wrong here?

            ...

            ANSWER

            Answered 2022-Feb-10 at 08:03

            You'll need to define the node position by setting the arrangement argument to stop plotly from automatically justifying the position.

            This requires some finessing as you need to specify the coordinates of the nodes. You can find more details here: https://plotly.com/python/sankey-diagram/#define-node-position

            Code

            Source https://stackoverflow.com/questions/71049211

            QUESTION

            Get the request header in Plotly Dash running in gunicorn
            Asked 2022-Feb-01 at 08:20

            This is related to this post but the solution does not work.

            I have SSO auth passing in a request header with a username. In a Flask app I can get the username back using flask.request.headers['username']. In Dash I get a server error. Here is the Dash app - it is using gunicorn.

            ...

            ANSWER

            Answered 2022-Feb-01 at 08:20

            You can only access the request object from within a request context. In Dash terminology that means from within a callback. Here is a small example,

            Source https://stackoverflow.com/questions/70935643

            QUESTION

            JupyterDash app.run_server error using Jupyter Notebook
            Asked 2022-Jan-31 at 12:23

            I am trying to make charts using JupyterDash but first things first... i can't run simple JupyterDash test via Jupyter Notebook because every time i receive the same error:

            ...

            ANSWER

            Answered 2022-Jan-30 at 20:52

            I had the same problem with and old notebook, after some changes, it works again.

            Initially, I had the code below:

            Source https://stackoverflow.com/questions/70908709

            QUESTION

            Dash Python - Making subplots when multiple parameters are selected
            Asked 2022-Jan-31 at 10:57

            I am trying to make an interactive plot where a user would select a location, then a time, and then one of a list of parameters. I am able to plot a basic plot of each parameter, but what I want to do is that when multiple parameters from the list are selected, a stacked subplot begins to form for each parameter. I have what I thought was a loop that is correct, but it doesn't seem to run through it to make the subplots.

            Looking for some help on how to do add subplots under the conditions of more than one parameter selected.

            Code below:

            ...

            ANSWER

            Answered 2022-Jan-31 at 10:57

            As per my research, it's not possible to generate a single plot the way you would like to. If you take a look at the plotly subplots documentation, you'll notice that subplots can only be populated with traces that are graph objects. The px.scatter() figure you're generating for a single parameter is already made up of multiple traces. A subplot cannot be populated with figures, only traces.

            First, I adjusted your code to produce subplots. Disregarding your dataframe manipulation and only focusing on the plotly syntax, there are some errors I found in this part:

            Source https://stackoverflow.com/questions/70886359

            QUESTION

            Plotly JupyterDash is not removing irrelevant columns when applying categoryorder sort to measure with a negative value
            Asked 2022-Jan-11 at 17:30

            I'm trying to sort the axis of my chart based on the values in the "sales" column. Once I apply fig.update_layout(yaxis={'categoryorder':'total descending'}) to my figure, the chart no longer removes irrelevant rows when filtering the dataframe by selecting the "099" value for the RadioItems callback option.

            code to recreate issue:

            ...

            ANSWER

            Answered 2022-Jan-11 at 17:30

            I was able to work around this issue by computing the ranking independently of the graphing step and placing the rankings into a series, rankings. I then passed the ranked series to

            Source https://stackoverflow.com/questions/70041819

            QUESTION

            How to use clickable map as a filter for line chart?
            Asked 2021-Dec-27 at 07:15

            I am new to Plotly Dash. I created some Dashboard in Tableau, in Tableau I have a dashboard with a map and a line chart next to it where I can select locations on the map and the line chart shows me the time series line chart from that sensor. I try to do this in Dash and learn some new tools like Dash since I often used Plotly with its beautiful graphs.

            I have internal data on a database with some complex logic where I have the locations on a seperate file, since I want to have as less data as possible I don’t want to include lat und lon in the SQL View. For this question I use data available on the web.

            I have sensor measuremt data like no2, no, o3 and more from sensors at different locations. My goal ist to have a map with the locations of the sensors. When I click on a location it should show me the line chart and I want to be able to select as many locations as I want so that I can compare the line charts.

            Is this possible? I have the line chart, but I can’t connect the part with the map to work. I will use this as a foundation to include many more graphs like bar charts and so on. The top selector will be a dropdown to select the parameter like no2, pm25. Many thanks in advance.

            This is the line chart so far:

            ...

            ANSWER

            Answered 2021-Dec-27 at 07:15

            If you are not bound to use a Graph component for the map, the Map component from dash-leaflet supports click events natively. Here is a small example, where map clicks are used to update a graph,

            Source https://stackoverflow.com/questions/70474999

            QUESTION

            Another dash/plotly dilemma
            Asked 2021-Dec-23 at 22:18

            I hate to keep posting about dash\plotly but I cant understand what is going wrong here. I have copied and pasted from the plotly site the code in order to display a pie chart with a drop down menu. When I create the dashboard there is a dropdown menu that shows all the categories but there is no pie chart to be seen. Please help me to understand what is going wrong. Code below:

            ...

            ANSWER

            Answered 2021-Dec-23 at 22:18

            I think the main issues with your code were that your generate_chart function had two arguments, but the @app.callback decorator had only one input argument, and that for the values argument in px.pie, you need to pass a column name whose values can be summed together. One issue with using px.pie in this case is that if you sum the values in the 'class' column, the 0s for success will always sum to 0.

            Since you explained in your comment that what you really want to display in your pie chart is the count of successes and failures (which are 0s and 1s in the 'class' column), I thought it would be easiest to sum up the number of 0s and 1s for the particular 'Site', and pass the arguments labels=['success','failure'] and values=[success_count, failure_count] to go.Pie.

            Source https://stackoverflow.com/questions/70453867

            QUESTION

            Progress pie chart subplot with percentage
            Asked 2021-Dec-22 at 16:01

            I'm trying to make a donut chart with percentage of completion. Below is my code:

            ...

            ANSWER

            Answered 2021-Dec-22 at 13:53

            I haven't checked it in the dash environment, but I did check it plotly. The annotations in the subplot set the respective values in the list. See this in the official reference.

            Source https://stackoverflow.com/questions/70447064

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install DCC

            You can download it from GitHub.
            You can use DCC like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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